diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
new file mode 100644
index 0000000..f3ecfd3
--- /dev/null
+++ b/.github/workflows/documentation.yml
@@ -0,0 +1,80 @@
+name: Build & Deploy Documentation
+
+on:
+ workflow_run:
+ workflows: [Algorithm Analysis]
+ types:
+ - completed
+permissions:
+ contents: read
+ pages: write
+ id-token: write
+jobs:
+ build:
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+ - name: Setup Pages
+ uses: actions/configure-pages@v4
+ - name: Set up Python
+ id: setup_python
+ uses: actions/setup-python@v5
+ with:
+ python-version: "3.11"
+ - name: Cache pip
+ uses: actions/cache@v3
+ id: pip-cache
+ with:
+ key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+ path: ${{ env.pythonLocation }}
+ if: steps.pip-cache.outputs.cache-hit != 'true'
+
+ - name: Install dependencies
+ run: |
+ pip install -r requirements.txt
+
+ # Action to download artifacts from a different workflow (analysis.yml)
+ - name: 'Download artifact'
+ if: ${{ github.event.workflow_run.conclusion == 'success' }}
+ uses: actions/github-script@v6
+ with:
+ script: |
+ let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+ owner: context.repo.owner,
+ repo: context.repo.repo,
+ run_id: context.payload.workflow_run.id,
+ });
+ let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+ return artifact.name == "Figures"
+ })[0];
+ let download = await github.rest.actions.downloadArtifact({
+ owner: context.repo.owner,
+ repo: context.repo.repo,
+ artifact_id: matchArtifact.id,
+ archive_format: 'zip',
+ });
+ let fs = require('fs');
+ fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/Figures.zip`, Buffer.from(download.data));
+
+ - name: 'Unzip artifact'
+ run: unzip Figures.zip
+
+ - name: Build html
+ run: |
+ mkdir docs/_static
+ mv *.pdf docs/_static/
+ sphinx-apidoc -o docs src
+ cd docs/
+ make html
+
+ - name: Upload docs artifact
+ uses: actions/upload-pages-artifact@v3
+ with:
+ path: 'docs/_build/html'
+
+ - name: Deploy to GitHub Pages
+ id: deployment
+ uses: actions/deploy-pages@v4
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..41c270b
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..e268db2
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(".."))
+
+project = 'TF2.4 IVIM MRI Code Collection'
+copyright = '2024, OSIPI'
+author = 'OSIPI team'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc"]
+
+templates_path = ['_templates']
+exclude_patterns = ['Thumbs.db', '.DS_Store']
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = False
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = False
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
diff --git a/docs/figures.rst b/docs/figures.rst
new file mode 100644
index 0000000..1291f6a
--- /dev/null
+++ b/docs/figures.rst
@@ -0,0 +1,45 @@
+Algorithm Analysis Figures
+===========
+
+.. raw:: html
+
+
+
+
+
+
+ Algorithm Analysis Figures
+
+
+
+ Diffusion grid for limited algorithms:
+